Comparison of gene expression profiles among papilla, medulla and cortex in rat kidney
Comparison of gene expression profiles among papilla, medulla and cortex in rat kidney
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DOI：
10.2131/jts.31.449
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发表时间：
2006-12-01
影响因子：
2
通讯作者：
Urushidani, Tetsuro
中科院分区：
文献类型：
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作者：
Tamura, Kotaro;Ono, Atsushi;Urushidani, Tetsuro
本研究的目的是比较不同肾脏区域的基因表达谱，作为毒理基因组学的基础。将大鼠肾脏分为乳头、髓质和皮质，并从这些和整个切片中分离总RNA。基因表达谱分析使用Affyssin Rat Genome 230 2.0 Array进行。当应用全局归一化时，β-肌动蛋白或GAPDH的表达在区域之间变化。认为不能进行这种比较，特别是在乳头和其他部分之间，因为前者的总mRNA产量相对较低。事实上，对乳头、髓质、皮质和整个切片中的基因表达值进行方差分析，并且基因的数量似乎在乳头中最高。还观察到许多基因在整个切片中显示出最大值或最小值，这在理论上是不可能的。为了克服与全局标准化相关的问题，采用“percelome”标准化（一种获得与每个细胞的mRNA拷贝直接相关的值的方法）来比较区域。在应用该程序时，通过ANOVA有效地提取了具有区域表达差异的探针集。当它们按与其他区域的倍数差异排序时，较高的等级被肾脏功能的特征基因占据，即，通道、转运蛋白和代谢酶。其中一些与文献一致，并与病理生理现象有关。对肾脏解剖区域基因表达数据的全面比较，将大大加强对肾脏生理功能和毒性机制的研究。
The aim of this study was to compare gene expression profiles in the different kidney regions as the basis for toxicogenomics. Rat kidney was separated into papilla, medulla and cortex, and total RNA was isolated from these and from the whole slice. Gene expression profiling was performed using Affymetrix Rat Genome 230 2.0 Array. When global normalization was applied, the expression of beta-actin or GAPDH varied among the regions. It was considered that such a comparison could not be made, especially between papilla and other portions, since the production of total mRNA in the former was relatively low. In fact, ANOVA was performed on the gene expression values with global normalization in papilla, medulla, cortex, and whole slice, and the numbers of genes appeared to be the highest in papilla. It was also observed that many genes showed their maximum or minimum in the whole slice, which was theoretically impossible. To overcome the problems associated with global normalization, the "percelome" normalization (a way to obtain the values directly related to the copies of mRNA per cell) was employed to compare the regions. In applying this procedure, probe sets with regional difference in expression were efficiently extracted by ANOVA. When they were sorted by the fold difference to other regions, the higher rank was occupied by genes characteristic of the functions of kidney, i.e., channels, transporters and metabolic enzymes. Some of them were consistent with the literature and were related to pathophysiological phenomena. Comprehensive comparison of data of gene expression in the renal anatomical area will greatly enhance studies of the physiological function and mechanism of toxicity in kidney.